Sodium in PDB 8rwl: Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1

All present enzymatic activity of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1:
1.1.1.299;

The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1, PDB code: 8rwl was solved by S.Coquille, J.Roche, S.Engilberge, E.Girard, D.Madern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.25, 78.25, 251.3, 90, 90, 90
R / Rfree (%)	20.4 / 24.3

The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1 (pdb code 8rwl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1, PDB code: 8rwl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:61.6 occ:1.00 O A:HOH524 2.1 61.4 1.0 HB2 A:ALA60 2.4 71.1 1.0 O A:VAL27 2.5 66.0 1.0 O A:ASP59 2.7 72.2 1.0 O A:LEU24 2.9 53.3 1.0 O A:ALA22 2.9 49.9 1.0 O A:HOH510 2.9 69.2 1.0 CB A:ALA60 3.3 59.1 1.0 HB1 A:ALA60 3.6 71.1 1.0 C A:VAL27 3.7 63.6 1.0 C A:ASP59 3.8 69.0 1.0 HA A:ASP25 3.9 78.6 1.0 HA A:ALA60 3.9 74.5 1.0 HB3 A:ALA60 3.9 71.1 1.0 C A:ALA22 3.9 52.0 1.0 HA A:ASN28 3.9 69.2 1.0 C A:LEU24 3.9 53.7 1.0 HB A:VAL27 4.0 78.1 1.0 CA A:ALA60 4.0 62.0 1.0 HG3 A:LYS58 4.2 86.5 1.0 HA A:ALA22 4.3 58.9 1.0 H A:VAL27 4.3 87.3 1.0 N A:ALA60 4.3 57.5 1.0 HG2 A:LYS58 4.5 86.5 1.0 HA A:LEU23 4.5 61.5 1.0 C A:LEU23 4.5 48.1 1.0 HG12 A:VAL27 4.6 72.0 1.0 CA A:ASP25 4.6 65.3 1.0 CA A:VAL27 4.6 73.8 1.0 N A:LEU24 4.6 53.9 1.0 O A:LEU23 4.6 52.6 1.0 O A:ASP25 4.6 64.9 1.0 N A:ASN28 4.6 57.1 1.0 HB3 A:LYS58 4.6 69.9 1.0 CA A:ASN28 4.7 57.5 1.0 HD22 A:LEU53 4.7 60.8 1.0 CB A:VAL27 4.7 64.9 1.0 N A:VAL27 4.7 72.6 1.0 CA A:ALA22 4.7 49.0 1.0 N A:ASP25 4.7 57.6 1.0 CG A:LYS58 4.7 71.9 1.0 C A:ASP25 4.7 61.8 1.0 H A:ASP59 4.7 75.8 1.0 N A:LEU23 4.7 46.2 1.0 CA A:LEU23 4.8 51.1 1.0 H A:LEU24 4.8 64.8 1.0 N A:ASP59 4.9 63.1 1.0 CA A:LEU24 4.9 48.2 1.0 CA A:ASP59 4.9 62.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:47.5 occ:1.00 O B:ASP59 2.3 45.3 1.0 O B:VAL27 2.5 42.6 1.0 O B:HOH526 2.5 43.7 1.0 O B:LEU24 2.5 44.7 1.0 O B:ALA22 2.6 40.8 1.0 HB2 B:ALA60 2.7 58.1 1.0 O B:HOH559 2.8 56.0 1.0 C B:ASP59 3.5 46.2 1.0 HA B:ASP25 3.6 61.1 1.0 C B:LEU24 3.6 45.3 1.0 C B:VAL27 3.6 40.9 1.0 H B:ASP59 3.7 56.1 1.0 CB B:ALA60 3.7 48.3 1.0 C B:ALA22 3.7 42.1 1.0 HB B:VAL27 3.9 48.8 1.0 HA B:ASN28 3.9 55.6 1.0 HA B:ALA60 4.0 62.2 1.0 H B:VAL27 4.0 54.2 1.0 HB1 B:ALA60 4.1 58.1 1.0 O B:LEU23 4.1 46.1 1.0 C B:LEU23 4.1 44.2 1.0 HA B:ALA22 4.2 49.8 1.0 CA B:ALA60 4.2 51.6 1.0 HB3 B:ALA60 4.3 58.1 1.0 N B:ALA60 4.3 53.4 1.0 N B:LEU24 4.3 37.5 1.0 CA B:ASP25 4.3 50.8 1.0 HB3 B:LYS58 4.3 52.5 1.0 N B:ASP59 4.4 46.6 1.0 N B:ASP25 4.4 44.0 1.0 CA B:VAL27 4.5 44.6 1.0 N B:VAL27 4.5 45.0 1.0 HA B:LEU23 4.5 49.0 1.0 CA B:ASP59 4.6 50.9 1.0 H B:LEU24 4.6 45.2 1.0 CA B:LEU24 4.6 43.9 1.0 CA B:ALA22 4.6 41.4 1.0 CB B:VAL27 4.6 40.5 1.0 O A:HOH525 4.6 64.3 1.0 N B:ASN28 4.6 41.9 1.0 HD22 B:LEU53 4.6 64.2 1.0 C B:ASP25 4.6 50.9 1.0 N B:LEU23 4.6 38.3 1.0 HG12 B:VAL27 4.6 53.1 1.0 CA B:LEU23 4.7 40.7 1.0 CA B:ASN28 4.7 46.2 1.0 O B:ASP25 4.8 47.1 1.0 HB1 B:ALA22 4.9 48.2 1.0 HB3 B:ASP59 4.9 66.7 1.0 HB2 B:LEU24 5.0 59.5 1.0 O B:LEU21 5.0 42.4 1.0

S.Coquille, C.Simoes Pereira, C.Brochier-Armanet, J.Roche, G.Santoni, N.Coquelle, E.Girard, F.Sterpone, D.Madern. Navigating the Conformational Landscape of An Enzyme. Stabilization of A Low Populated Conformer By Evolutionary Mutations Triggers Allostery Into A Non-Allosteric Enzyme. To Be Published.